Having replaced Locking Block and Outer Barrel the M9 PTP will not go back together.

The rod with the spring will not line up with the inside of the gun.

Suggestions?

Are you talking about the spring guide not going into the front hole of the slide? If so, just go slow and it will fit.
If you're talking about the slide not going back on to the frame when everything is assembled in the slide, try turning the gun upside down with the grip pointing toward the sky. Then try sliding it back into battery. Thats how its worked for me, so far....